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Integrating molecules, morphology and fossils: the evolution of booid snakes as revealed by tip-dating total-evidence phylogenetics

Grant number: 19/11166-3
Support Opportunities:Scholarships abroad - Research Internship - Doctorate
Effective date (Start): October 01, 2019
Effective date (End): September 29, 2020
Field of knowledge:Biological Sciences - Zoology - Paleozoology
Principal Investigator:Annie Schmaltz Hsiou
Grantee:Silvio Yuji Onary Alves
Supervisor: Michael Lee
Host Institution: Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil
Research place: Flinders University, Australia  
Associated to the scholarship:17/00845-1 - Origins and macroevolution of Booidea (Squamata, Serpentes) using phylogenetic and ancestral area reconstruction analysis, BP.DR


Snakes constitute an ecologically and taxonomically diverse group of squamates, with more than 3000 living species distributed across all continents except Antarctica. In the past few decades several phylogenetic hypotheses have been proposed for snakes, both regarding their placement within Squamata and the details of their ingroup relationships. These hypotheses were initially based on either morphological (i.e. osteology) or molecular (DNA) data, and often these methods produced strikingly different scenarios. Both of these approaches have limitations, most notably, molecular analyses cannot incorporate important information from the fossil record (fossil snakes), while morphological analyses rely on much more limited amounts of data, which in turn also prevents accurate estimates of rates of evolution and dating of ancestral nodes. For these reasons, some of the most recent studies have attempted to combine molecular and morphological data, in order to produce more robust evolutionary hypotheses. However, several issues still persist that may hamper our understanding of snake phylogenetic relationships, as indicated by the poor resolution so far obtained especially within the booid radiation (boas and pythons), which traditionally have been poorly sampled in morphological datasets. The main goal of this project is to integrate the molecular data and the morphological information (i.e. fossil record and osteology) from living and extinct snakes, and rely on tip-dating methods to generate a new Bayesian total-evidence phylogenetic hypothesis with a special focus on resolving the relationships among lineages of booids. Morphological data from an increased sample of booid snakes (here including new undescribed exceptionally-preserved booid fossil material), combined with the available molecular data has certainly the best potential to solve these long-standing issues. These new results will provide new insights into the evolution of snakes, the dates of divergence of major lineages, their evolutionary rates, and the primary data for a new booid biogeographical quantitative analysis. Additionally, the purpose of this internship is to provide the applicant with the unique opportunity to train and learn new skills in Dr Michael Lee's laboratory at Flinders university, Australia, who is one of the leading experts in Bayesian phylogenetic analyses and methods. During this period the candidate will be trained in Bayesian inference methods with emphasis on total-evidence analyses, and expand the taxon sampling of booids by including several python species that are native to Australia and the surrounding regions, as well as some pivotal fossil snakes (madtsoiids). While in Australia, the candidate will also visit other local institutions where research on booids is currently being carried on (Dr Scott Keogh's lab at the Australian National University in Canberra), in order to expand his network of potential collaborators and possibly learn additional skills (e.g. geometric morphometrics). This internship will be of vital importance to increase the candidate skills, knowledge, and international network of collaborators; will provide a unique opportunity to train the student in an innovative multidisciplinary research area, and will undoubtedly have positive implications to his career and eventually the study of paleontology in Brazil.

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Scientific publications
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
FACHINI, THIAGO SCHINEIDER; ONARY, SILVIO; PALCI, ALESSANDRO; LEE, MICHAEL S. Y.; BRONZATI, MARIO; HSIOU, ANNIE SCHMALTZ. Cretaceous Blind Snake from Brazil Fills Major Gap in Snake Evolution. ISCIENCE, v. 23, n. 12, . (18/18145-9, 17/00845-1, 11/14080-0, 19/11166-3)
ONARY, SILVIO; HSIOU, ANNIE S.; LEE, MICHAEL S. Y.; PALCI, ALESSANDRO. Redescription, taxonomy and phylogenetic relationships of Boavus Marsh, 1871 (Serpentes: Booidea) from the early-middle Eocene of the USA. JOURNAL OF SYSTEMATIC PALAEONTOLOGY, v. 19, n. 23, p. 22-pg., . (17/00845-1, 19/11166-3)

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